The Doctor's Daughter
by Krystal-Enderheart
Summary: The 11th Doctor, Amy and Rory take a trip to 19th Century Japan, but they come home with more than they bargained for. What they find, means The Doctor must visit an old friend to keep it safe, and much is learnt that day.


"Ah! Japan! I've always wanted to come to Japan, nice place, weird food," The Doctor said as he burst out the doors of the TARDIS and looked around, keeping one hand on the blue, wooden exterior.

"Japan!" Amy said, stepping out wearing a rather bright red jumper with a blossom pattern, skinny jeans and pumps.

"Sorry, why are we in Japan?" Rory asked, pulling his jacket over his blue t-shirt.

"Because! We can be," The Doctor said, turning to face them in the snow. It was winter.

"Amy, you look lovely, Rory... Very..." He paused and made random, wild hand gestures. "Rory," He finished.

"Thank you," Amy said, curtsying. "Remind me, why do you have this in your wardrobe?" She asked, looking down at the jumper.

"Uh, I kept it spare. Me and the Empresses of Japan, long story," He explained.

"Wait, did you say I look "very Rory"? What does that even mean?" He asked, watching the Doctor start to run off, the pair of companions running after him.

The Doctor. Always running, he was. Never stops with the running.

"So, where to first, Doctor?" Amy asked.

He was scanning discreetly with his sonic screwdriver while Rory sat on the stone wall of a nearby rock garden. The garden had a seemingly impossible stack of rocks in the middle of a pond, with water cascading over it into a frozen pool full of large koi of varying colours. The Doctor turned in a circle, as he always did, and finally turned to face them with _that_ smile on his face.

"Come along Pond!" He said with glee, and grabbed her wrist, running off down a supposedly random path. Rory following closely behind, really wishing he wouldn't do this.

"Why isn't anyone noticing you?" Rory asked over The Doctor's shoulder.

He was holding his sonic screwdriver in his hand, held up to his face, and it was making loud bleeps. Occasionally he'd straighten his bow tie, but most of the time he held his other hand up in the air, one finger being licked and held aloft.

"Perception filter. Affecting all of us, why no one's staring at you talking to me over my shoulder," He almost whispered.

And then suddenly stopped as the bleeps turned into a continuous sound.

"What's wrong? Where? Oh. Oh! OH!" The Doctor started whispering, eventually shouting. He started running again.

Always running. Why did it have to be running?

* * *

"Doctor?! What is it?!" Amy asked worriedly, running beside him.

Only then did she notice the smile of pure delight on his face. Not the one he had when he found the solution to a bad situation, genuine joy. It was kind of weird. Never had she, in her entire time travelling with him, ever seen him quite like this.

"We're going to find a friend!" He called back over his shoulder.

"One of your friends?! You don't mean archenemy by that, do you?!" Rory screamed forwards to him.

"No! I mean an actual..." He paused as they slowly and gradually ground to a halt."...friend," He finished.

They were at the bottom of a fairly dark alleyway. Damp, moss-coated stone walls and a rat's squeaks. But at the feet of The Doctor, lay the most impossible sight, even by his standards. A 12 year-old girl lay unconscious in the snow and barely breathing, her clothes from the 21st century but torn, muddy and too small. Long, matted, brown hair clung to her wet face, and the tiniest of faint glows came from under her eyelids, barely noticeable. She was littered with small cuts and scrapes, some of them still bleeding and staining the snow below them red.

"Oh my god," Amy said, rushing to get past him, though The Doctor held his arm out to stop her.

"She's fine." All he said while he scooped the young girl up carefully in his arms. "We need to get her back to The TARDIS,"

"What? Why? What's so special about her? She's probably just some homeless kid," Rory said, following The Doctor as he stand in the journey back.

"Rory!" Amy shouted in a whisper.

"Rory Williams, she. Is not. Just. Some. Homeless kid," He said with cold in his voice, coming rather close to the centurion's face.

"Well then, who is she?" He asked as they approached the doors to the blue box.

The Doctor clicked his fingers and the doors swung open. He raced inside and gently laid her on the floor, turning his attention to the main console. Amy and Rory wandered in, and leaned against the railings, watching the madman work. After a while, he stopped and calmly walked over to the girl, still unconscious. He took out his sonic screwdriver, and scanned her with it. He looked at the reading himself, before plugging it into the console.

"So? What's all this for?" Amy asked, breaking the silence.

"Well, I need to know what she is. My screwdriver didn't know," He replied, pulling the screen around to him.

"Okay, so what does the TARDIS say?" She tried.

The Doctor fell silent for a moment, staring in disbelief at the screen before bursting into life and running round to hug his companions. When he let them go, his face had lit up like a Christmas tree.

"So?" Rory asked tentatively.

"She's a Time Lord," He said, practically bursting with joy.

"She's what?" He didn't understand. "I thought you were the last one."

"I was! Then, I found her," The Doctor said, sitting on the floor beside the girl.

"Wait, if she's a Time Lord, shouldn't she be regenerating or something?" Amy asked.

The Doctor turned around to face her, then looked at Rory. "These are the questions you need to ask. I love it when you ask those questions Amy, you're such a clever clogs!"

"Still doesn't answer my question. Why isn't she regenerating?"

"She can't." His answer was blunt, and gave no more information.

"What do you mean, 'she can't'?" Rory asked.

"She can't. She can't regenerate. She's in such a bad shape, she's dying. Starting a regeneration cycle is painful, you know. Her body knows she couldn't take the pain, she would die from it," He explained, pulling the hair from her face.

"So, what now then?" Amy asked.

"We fix her! Heal some cuts, bring her conscious again, that sort of stuff!" He exclaimed, jumping to his feet.

"Well, that's easy, then. Have you got a medkit on the TARDIS?" Rory asked.

"Have I got a medkit on the TARDIS? Of course I've got a medkit on the TARDIS!" He paused, looking around. "Somewhere," He added.

"Great," He said sarcastically, leaning back against the railings.

"Anyway, she's a Time Lord. She may not be able to regenerate, but she can use regenerative energy to repair herself over time," He said, looking to the girl. He hadn't noticed before, but she was exceedingly skinny. Her ribs were visible, and her breaths shallow. "On the other hand, she does need food,"

"Food?" Amy questioned. "Is this gonna be like you with fish fingers and custard? You know, that veterinary bill cost a lot,"

"What bill? And no," He answered, pressing buttons on the console.

"Remember when you chucked out the bread and butter? It hit my neighbour's cat. They made me pay the bill," Amy explained.

"Oo, sorry. Yes, I do remember,"

"What are you doing?" Amy asked, watching him dance around the console.

"What?" He looked up.

"I said, what are you doing?" She repeated.

"Oh, right. I'm going somewhere safer for her," He explained.

The TARDIS stated to make the noise it always did as they took off, but managed to stay relatively stable. Amy walked over and sat by the side of the girl, holding her steady so she wouldn't bump into anything or slide around.

"So, where are we?" She asked, standing up and walking over to the doors.

The Doctor gently picked the girl up, watching as her skin gently glowed and healed some of the smaller cuts. He nodded for Amy to open the doors, and Rory followed behind The Doctor.

"This is just some street! How is this safe for her?" Amy asked.

"Not just 'some street'. Bannerman Road. Go knock on that door over there, the big house, number 13" He said, gesturing towards a house on his right.

They all walked over, and Amy knocked. A young boy answered the door, around 14, wearing a blue t-shirt and jeans.

"Hello Luke. I might have changed since we last met. Where's Sarah Jane?" The Doctor asked.

"Oh, you're-! Oh! Hang on!" Luke said, into the house. "Mum!" He called up. "It's The Doctor!"

Sarah Jane came rushing down the stairs, and when she saw The Doctor, nearly cried. "I take it you're staying for a while?" She asked as her eyes travelled to the girl in his arms.

"Yes. Sarah Jane, Luke, this is Amy and Rory," He introduced them.

"And who's the girl you're holding?" Sarah Jane asked, shutting the door behind them.

"We don't know," Amy answered.

"What? What do you mean you don't know?" She asked, walking over to look at the girl herself. When she saw the regenerative energy, her eyes widened. "Is she-?"

"Yes. A Time Lord, like me. Though, she can't regenerate, it would tear her apart. She needs food, she hasn't eaten for days," The Doctor explained.

"Well, what kind of food? I've heard the infamous story of you and fish custard," She asked with a smile.

"Really, probably soup," He answered, walking through to the living room and laid the now shaking girl on the sofa. It looked like it was becoming increasingly difficult for her to breath.

The girl's breathing had become more steady, and she had stopped shaking. Most of her cuts were healed, but she was still unconscious. Sarah Jane had laid some blankets over her, and put a spare pillow behind her head to try and make her comfortable.

"Rory. You're a nurse, how do you wake up someone that's unconscious?" Amy asked her husband.

"Well, there isn't a way really. Just make sure they're breathing fine, and wait," He answered with a shrug.

"Okay, Doctor? You've got a degree in everything, and you're both Time Lords, do you know anything?" She tried.

"Actually, Rory's right. Having an extra heart doesn't make much of a difference when it comes to unconsciousness," He replied.

"Where did you find her?" Luke asked, peering round Rory to look at her.

"19th Century Japan," Rory answered. "In an alleyway,"

The Doctor was sat beside her, with a small smile on his face, brushing her hair. It was greasy, and had countless things in it, but he brushed it just the same. She looked peaceful with him by her side, and every now and again you could see the smallest hint of a smile on her face.

"Doctor?" Sarah Jane asked him.

"Hm?" He asked, looking up to face her.

"Do you recognise her? If she's a Time Lord, surely she was back on Gallifrey?"

He shook his head. "She's too young. Even for a Time Lord. For the first 40 or so years of our lives, we grow and age at the same rate humans do, then stop ageing physically. She really is just 12. Gallifrey has been gone for centuries. I wonder who her parents were?"

"Could her parents still be out there? You know, more Time Lords?" Amy asked.

"No. I keep the TARDIS looking for Time Lord life signatures throughout all of space and time. That's how I found her. There was only one life signature," The Doctor explained with sadness in his voice.

All of a sudden, a quiet groan came from the girl, and her eyes gently fluttered open. She rolled her head to look up at the Doctor.

"W-Where... Am...I?" She whispered with struggle.

"It's okay, don't try and talk. You'll be fine," He reassured her, helping her to sit up slightly.

She moaned in reply, giving a small nod of her head.

"I'm The Doctor, this Amy, Rory, Luke and Sarah Jane. Can you tell me your name?" He asked.

"I-I'm...The...Ar-Artist..." She breathed, moving her hand towards The Doctor.

"Oh, so you've chosen. Tell me, Artist, have you looked into the untempered schism yet?" He asked her.

She gently nodded. "I chose my name because I want to create something with meaning. Not everyone understands me, but those who do would appreciate it," She explained.

Amy bent down beside her. "Artist, how old are you? If you don't mind me asking."

"I'm 12. How old are you, Doctor?" She asked.

He smiled. "Nearly 1200. It's been a while for me. I bet you haven't regenerated yet, have you?"

She shook her head, then looked at her hands. They were glowing quite vibrantly now. "First time for everything," She said shakily.

The Doctor nodded and stood, along with Amy. They stepped back a bit, and watched as the glowing got brighter. The Artist looked into The Doctors eyes and he saw she was scared. Terrified, even. He smiled at her to try and give her reassurance, but he knew how much it might hurt.

All the five of them could do was stand by and watch as she cried out in pain, regenerative energy bursting from her body. When it faded, she slowly sat up and looked up at them. She reached a hand out towards The Doctor, and he stepped forward, bending down to her height.

"You are extraordinary," He commented, noting that her appearance hadn't changed. "How did you keep your appearance?"

"I-I don't know. It hurt though, and I think- argh!" She cried out, grabbing at where her right heart was. She fell backwards against the sofa, and brought her knees to her chest.

The Doctor sat beside her on the sofa and put an arm around her. "It's okay, that's normal. It's the excess energy trying to escape, let it," He explained. She relaxed and breathed out, the regenerative energy escaping with her breath. She smiled as she watched the golden sparkles dance around. Then out of the blue, she wrapped her arms around The Doctor in a hug. He laughed and smiled, wrapping his arms around her.

"So, what now?" Amy asked.

The two Time Lords looked at each other, then at Amy and the others. "Can I come exploring with you?" The Artist asked.

Amy and Rory looked at The Doctor, and he just nodded. "Of course you can, Artist. I happen to have a TARDIS,"

"Really? What's that?" She asked with a smile.

His smile faded and he breathed out. "Okay, general background," He said to himself, then hit his head against hers. They both cried out in pain.

"I have two hearts?!" She exclaimed.

The Doctor ignored her, and breathed out again. "Specific details," He said, and they hit heads again.

"You stole a Type 40 TARDIS?!" She asked, her breathing heavy.

"Borrowed," He corrected her.

"Doctor, what did you do?" Rory asked.

"Data transfer. Nothing big, but it sure does hurt," He said, and the two Time Lords sat beside each other. "Sarah Jane, do you still have Mr Smith?"

"Of course I do, he's in the attic with K9," She answered.

"Can we go up there?" He asked.

"Yeah, yes, of course," She said.

The Doctor stood up, and held his hand out to The Artist. "Artist? Do you think you can stand?"

"I think so, and Doctor, you can call me by the name I use here on Earth instead of Artist,"

"Which would be?" He inquired.

"Crystal Smith," She answered.

"Well, Crystal, Let's go to the attic," Sarah Jane said with a smile.

Crystal took hold of The Doctor's hand and stood up slowly. Her legs were a little shaky, but she could stand. "Amy?"

"Yeah?" Amy responded, looking to the young girl.

"You're very pretty," She said with a smile. "I hope one of my regenerations looks like you,"

Amy laughed. "Thank you."

Crystal smiled and followed Sarah Jane and her son Luke up to the attic.

"Mr Smith, I need you," Sarah Jane said as she opened the door. Crystal followed, still holding The Doctor's hand.

The super computer appeared, without the fanfare. Though Clyde, Rani and Luke liked it, she insisted it be gotten rid of.

"How can I help, Sarah Jane?" He asked in his robotic voice.

"Mr Smith, you remember The Doctor? This is Amy and Rory, his current companions, and Crystal. She's a Time Lord," Sarah Jane introduced them all.

"Of course I remember The Doctor, though he has regenerated since I last saw him," Mr Smith remarked.

"Hello Mr Smith," The Doctor said, and Crystal waved at the computer.

"Sarah Jane, you said Crystal is a Time Lord. Could I please scan her? Having knowledge of a young Time Lord may prove useful," He remarked.

"Well, that's up to Crystal," She answered, looking to the young girl still clinging to The Doctor's hand.

"Will it hurt?" She inquired.

"No," Mr Smith answered.

"Okay then, if it'll help," She said, looking up at The Doctor. He smiled at her.

She stepped forward, towards the computer, letting go of The Doctor's hand as she did so. Her steps seemed less shaky than before. Mr Smith quickly scanned her, and a series of numbers appeared on the screen. Crystal immediately ran back to The Doctor and grabbed hold of his hand.

"Rory, have you noticed how she seems to always want to hold his hand?" Amy whispered in Rory's ear.

"I feel safe holding his hand," Crystal said, looking over her shoulder at the pair.

"How did you hear that?" Amy asked.

"How could I not? You weren't being particularly quiet," She answered.

Amy hummed, but Mr Smith interrupted.

"My scans show that Crystal's second heart started beating approximately half an hour ago, where as her primary heart has been beating rapidly all her life to compensate," He explained.

"Half an hour ago, wasn't that when we found her?" Rory asked.

"Yes, it was. But why would we trigger her second heart?" The Doctor mused.

"Maybe because you're a Time Lord?" Rory offered.

"No, no." The Doctor said. He looked at the girl still clutching his hand like her life depended on it. "Though maybe..."

"I recognise that face. That's your thinking face!" Sarah Jane exclaimed with a smile.

"But if Crystal's second heart only just started beating, how has she survived this long? I thought Time Lords needed two hearts to survive," Luke thought out loud.

"I've missed something, what was it? I know I missed something," The Doctor said under his breath, starting to zone out. After a while, he finally had it. "Ha! Of course!"

"Doctor?" Crystal asked.

"Yes, Crystal?" He said with a smile.

"You parked The TARDIS in the middle of Bannerman Road," She pointed out.

"Good point,"

"And you park it with the brakes on," She added.

"How would you know? You've never flown a TARDIS, you've never even seen one," He said, scrunching up his face.

"Trust me, I know," She said with a small smile.

The Doctor told Crystal to stay inside while he parked The TARDIS somewhere safer, and when he let go of her hand she rushed over to where Amy and Rory were sat on the sofa. She plopped down next to Amy and grabbed her hand, smiling up at the redhead.

"Your hands are /really/ warm," Amy commented.

"My hands have always been warm. They never seem to be cold, even if I'm holding snow," She replied.

"Why do like holding hands so much?" Luke asked.

Crystal looked at Luke with a smile. "It makes me feel safe. After 7 years on the streets of Japan, on my own, I don't ever want to be alone again. If I'm holding hands I know there's someone here even if I can't see them,"

The Doctor came running back up to the attic with a smile. "As I was saying before, I think I know why Crystal's second heart didn't start beating until half an hour ago,"

"Why?" Luke asked him.

"She didn't have a second heart until half an hour ago," He answered, sitting next to her.

"What? What do you mean? How is that possible?" Sarah Jane asked.

"Crystal, have you ever had a pocket watch?" The Doctor asked.

"Yes, I do have one," She answered, reaching into her pocket and pulling out a watch like The Doctor's.

"Have you ever opened it?"

"I-no. Come to think of it, I haven't. Should I have?" She asked.

"Doctor?" Amy asked wearily.

"It's alright Amy. And that's why she didn't have her second heart. It's a watch like mine, see?" He said, pulling out an identical pocket watch.

"How is that possible?" Crystal asked.

"The watches. They are used by Time Lords when they need to stop being a Time Lord for whatever reason. Time Lords can separate into a human body and a Time Lord consciousness. The watches contain the consciousness until they are opened by the former Time Lord, at which point they restore them to their natural form. Crystal had her Time Lord consciousness, and subsequent second heart, stored in the watch. When we found her, my sonic screwdriver accidentally opened the watch and the energy flowed back into her," He explained.

"How do you know all that?" Rory asked.

"Because. I did it once," He said.

"You were a human for a bit?" Amy asked with a smile.

The Doctor nodded, and looked at Crystal to make sure she was okay. The young girl seemed to be staring into space.

"Doctor?" Mr Smith suddenly said.

"Yes Mr Smith?" He asked, looking up at the computer and walking over.

"I ran over the data from my scan earlier, and compared it to a previous scan of you," He started.

"Why would you do that?" The Doctor asked with a smile.

"My results show that you and Crystal share the same genetic line," The computer finished.

"What do you mean?" He asked, his smile fading.

"Crystal is your daughter,"

Upon hearing this, Crystal stood up and walked over to the stunned man, and gently took hold of his hand. They looked at each other and she smiled.

"Hello Daddy," She said.

"You knew, didn't you? How long did you know?" The Doctor asked her.

"Since I saw you," She answered.

"Doctor?" Amy asked.

"Yes, Amy?"

"Is she my granddaughter?" She inquired.

"Mr Smith, scan Amy and compare her DNA to Crystal's," The Doctor ordered.

Doing so, Mr Smith started comparing his data.

"Crystal is indeed Amy's granddaughter," He concluded.

Crystal looked around the room. "Luke, you're adopted, aren't you?"

"Uh, yeah, I am," He said, walking over to her. "How did you know?"

"I can hear the difference in your blood. You and Sarah Jane have different blood types, but you still call her Mum," She answered.

"You can hear the difference in their blood?" Rory asked.

Crystal nodded. "When I was 5, I was about to starve and winter was coming, so I tried to steal some bread. The baker caught me though, and punched me, a nasty right wing. It turned me deaf in my right ear, but I found a broken hearing aid in the rubbish one day, and using an old battery, a broken earring and some paper clips, I fixed it. I kept adjusting it, until one day I found this burnt bit of metal with a blue bulb at the end. It had so many wires in it, and using the circuits from it I made my hearing the best it could be," She told.

"Did you say burnt and blue at the end?" The Doctor asked.

"Yes,"

"That sounds like my old sonic screwdriver,"

"It certainly was sonic," She said. "Not sure about screwdriver,"

"I can see the resemblance," Amy said. "Crystal, do you like bow ties?"

"Not for me to wear, but I think my Dad looks cool in bow ties. Bow ties are cool," She answered with a smile.

"Oh, she is just like you," Amy said, putting a hand on The Doctor's shoulder.


End file.
